src/jalview/bin/AppletParams.java

   1 package jalview.bin;
   2
   3 import jalview.gui.Preferences;
   4
   5 import java.util.HashMap;
   6 import java.util.Map;
   7 import java.util.Vector;
   8
   9 /**
  10  * Collection of all known applet tags from JalviewLite
  11  *
  12  * @author hansonr
  13  *
  14  */
  15 @SuppressWarnings("serial")
  16 public class AppletParams extends HashMap<String, String>
  17 {
  18
  19   private final static String[] params = { "alignpdbfiles",
  20       Preferences.ANNOTATIONCOLOUR_MAX, Preferences.ANNOTATIONCOLOUR_MIN,
  21       "annotations",
  22       "APPLICATION_URL", "automaticScrolling", "centrecolumnlabels",
  23       "debug", "defaultColour", "defaultColourNuc", "defaultColourProt",
  24       "embedded", "enableSplitFrame", "externalstructureviewer", "features",
  25       "file", "file2", "format", "heightScale", "hidefeaturegroups",
  26       "jalviewhelpurl", "jnetfile", "jpredfile", "label", "linkLabel_",
  27       "linkLabel_1", "linkURL_", "nojmol", "normaliseLogo",
  28       "normaliseSequenceLogo", "oninit", "PDBFILE", "PDBSEQ",
  29       "relaxedidmatch", "resolvetocodebase", "RGB", "scaleProteinAsCdna",
  30       "scoreFile", "separator", "sequence", "showAnnotation", "showbutton",
  31       "showConsensus", "showConsensusHistogram", "showConservation",
  32       "showfeaturegroups", "showFeatureSettings", "showFullId",
  33       "showGroupConsensus", "showGroupConservation", "showOccupancy",
  34       "showQuality", "showSequenceLogo", "showTreeBootstraps",
  35       "showTreeDistances", "showUnconserved", "showUnlinkedTreeNodes",
  36       "sortBy", "sortByTree", "tree", "treeFile", "upperCase",
  37       "userDefinedColour", "widthScale", "windowHeight", "windowWidth",
  38       "wrap", };
  39
  40   public AppletParams(Map<String, String> info)
  41   {
  42     for (int i = params.length; --i >= 0;)
  43     {
  44       put(params[i], info.get(params[i]));
  45     }
  46   }
  47
  48   public String getParam(String param, String def)
  49   {
  50     String val = get(param);
  51     return (val != null ? val : def);
  52   }
  53
  54   // <applet
  55   // code="jalview.bin.JalviewLite" width="140" height="35"
  56   // archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
  57   // <param name="permissions" value="sandbox"/>
  58   // <param name="file" value="uniref50.fa"/>
  59   // <param name="treeFile" value="ferredoxin.nw"/>
  60   // <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555;
  61   // D,E=5555FF"/>
  62   // <param name="sortByTree" value="True"/>
  63   // <param name="showSequenceLogo" value="true"/>
  64   // <param name="showGroupConsensus" value="true"/>
  65   // <param name="showFullId" value="false"/>
  66   // <param name="linkLabel_1" value="Uniprot"/>
  67   // <param name="linkUrl_1"
  68   // value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
  69   // <param name="linkLabel_2" value="EMBL-EBI Search"/>
  70   // <param name="linkUrl_2"
  71   // value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
  72   // <param name="APPLICATION_URL"
  73   // value="http://www.jalview.org/services/launchApp"/>
  74   // </applet>
  75   //
  76   public AppletParams(String outerHTML)
  77   {
  78     String[] tokens = outerHTML.split("<param");
  79     outerHTML = tokens[0];
  80     String code = getAttr(outerHTML, "code");
  81     if (!code.equals("jalview.bin.JalviewLite"))
  82     {
  83       return;
  84     }
  85     for (int i = tokens.length; --i > 0;)
  86     {
  87       String param = tokens[i];
  88       String key = getAttr(param, "name");
  89       if (key != null)
  90       {
  91         String value = getAttr(param, "value");
  92         System.out.println("AppletParams " + key + " = \"" + value + "\"");
  93         put(key, value);
  94       }
  95     }
  96     put("_width", getAttr(outerHTML, "width"));
  97     put("_height", getAttr(outerHTML, "height"));
  98     put("_id", getAttr(outerHTML, "id"));
  99     put("_name", getAttr(outerHTML, "name"));
 100     put("_archive", getAttr(outerHTML, "archive"));
 101     put("_code", code);
 102   }
 103
 104   public AppletParams()
 105   {
 106     // TODO Auto-generated constructor stub
 107   }
 108
 109   public static AppletParams getAppletParams(String[] args,
 110           Vector<String> vargs)
 111   {
 112     AppletParams appletParams = new AppletParams();
 113     String resourcePath = null;
 114     for (int i = args.length; --i > 0;) // > 0 is correct, not >=0
 115     {
 116       if (args[i].startsWith("name=\"Info.resourcePath\""))
 117       {
 118         resourcePath = getAttr(args[i], "value");
 119         if (resourcePath.length() > 0 && !resourcePath.endsWith("/"))
 120         {
 121           resourcePath += "/";
 122         }
 123         break;
 124       }
 125     }
 126     for (int i = 1; i < args.length; i++)
 127     {
 128       String arg = args[i].trim();
 129       if (arg.startsWith("name="))
 130       {
 131         String prefName = getAttr(arg, "name");
 132         String appletName = prefName.toLowerCase();
 133         String argName = prefName;
 134         String value = getAttr(arg, "value");
 135
 136         // note that Application arguments ARE case-sensitive, but
 137         // Applet.getParameter() is not.
 138
 139         switch (appletName)
 140         {
 141
 142         case "file":
 143           argName = "open";
 144           appletName = null;
 145           value = resourcePath + value;
 146           break;
 147         case "file2":
 148           argName = "open2";
 149           prefName = null;
 150           value = resourcePath + value;
 151           break;
 152         case "features":
 153         case "jnetfile":
 154         case "jpredfile":
 155         case "pdbfile":
 156         case "scorefile":
 157         case "sequence":
 158           // setting argName to null indicates that we want
 159           // JalviewAppLoader to take care of this.
 160           prefName = argName = null;
 161           value = resourcePath + value;
 162           break;
 163         case "tree":
 164         case "treefile":
 165           // setting appletName to null indicates that we want
 166           // Jalview.doMain to taken care of this as Jalview args
 167           argName = "tree";
 168           appletName = null;
 169           value = resourcePath + value;
 170           break;
 171
 172         // non-loading preferences
 173
 174         case "defaultcolour":
 175           prefName = Preferences.DEFAULT_COLOUR;
 176           break;
 177         case "defaultcolournuc":
 178           prefName = Preferences.DEFAULT_COLOUR_NUC;
 179           break;
 180         case "defaultcolourprot":
 181           prefName = Preferences.DEFAULT_COLOUR_PROT;
 182           break;
 183         case "annotationcolour_max":
 184           prefName = Preferences.ANNOTATIONCOLOUR_MAX;
 185           break;
 186         case "annotationcolour_min":
 187           prefName = Preferences.ANNOTATIONCOLOUR_MIN;
 188           break;
 189         case "enablesplitframe":
 190           prefName = Preferences.ENABLE_SPLIT_FRAME;
 191           break;
 192         case "centrecolumnlabels":
 193           prefName = Preferences.CENTRE_COLUMN_LABELS;
 194           break;
 195         case "sortby":
 196           prefName = Preferences.SORT_ALIGNMENT; // id, etc.
 197           break;
 198         case "normalisesequencelogo":
 199           prefName = Preferences.NORMALISE_CONSENSUS_LOGO;
 200           break;
 201         case "relaxedidmatch":
 202           prefName = Preferences.RELAXEDSEQIDMATCHING;
 203           break;
 204         case "scaleproteinascdna":
 205           prefName = Preferences.SCALE_PROTEIN_TO_CDNA;
 206           break;
 207         case "userdefinedcolour":
 208           argName = "colour";
 209           prefName = Preferences.USER_DEFINED_COLOURS;
 210           break;
 211         case "wrap":
 212           prefName = Preferences.WRAP_ALIGNMENT;
 213           break;
 214
 215         // implemented; not tested:
 216
 217         case "oninit":
 218           prefName = null;
 219           break;
 220         case "annotations":
 221           value = resourcePath + value;
 222           argName = null;
 223           break;
 224         case "hidefeaturegroups":
 225           // TODO
 226           break;
 227         case "pdbseq":
 228           argName = prefName = null;
 229           break;
 230         case "sortbytree":
 231           prefName = Preferences.SORT_BY_TREE;
 232           value = checkTF(value);
 233           appletName = null; // taken care of by Jalview
 234           break;
 235         case "format":
 236           break;
 237         case "alignpdbfiles":
 238           argName = prefName = null;
 239           break;
 240         case "separator":
 241           break;
 242
 243         // TODO: probably not relevant?
 244
 245         case "rgb":
 246           prefName = null; // TODO no background for application?
 247           break;
 248         case "externalstructureviewer":
 249           break;
 250         case "application_url":
 251           break;
 252         case "automaticscrolling":
 253           break;
 254         case "heightscale":
 255           break;
 256         case "jalviewhelpurl":
 257           break;
 258         case "label":
 259           break;
 260         case "linklabel_":
 261           prefName = "linkLabel_";
 262           break;
 263         case "linklabel_1":
 264           prefName = "linkLabel_1";
 265           break;
 266         case "linkurl_":
 267           prefName = "linkURL_";
 268           break;
 269
 270         // unknown:
 271
 272         case "nojmol":
 273         case "normaliselogo":
 274         case "resolvetocodebase":
 275         case "uppercase":
 276         case "widthscale":
 277         case "windowheight":
 278         case "windowwidth":
 279           argName = prefName = null;
 280           break;
 281
 282         // TRUE/FALSE
 283
 284         case "debug":
 285           value = checkTF(value);
 286           break;
 287         case "embedded":
 288           value = checkTF(value);
 289           break;
 290         case "showbutton":
 291           value = checkTF(value);
 292           break;
 293         case "showannotation":
 294           prefName = Preferences.SHOW_ANNOTATIONS;
 295           value = checkTF(value);
 296           break;
 297         case "showconsensus":
 298           prefName = Preferences.SHOW_CONSENSUS_LOGO;
 299           value = checkTF(value);
 300           break;
 301         case "showconsensushistogram":
 302           prefName = Preferences.SHOW_CONSENSUS_HISTOGRAM;
 303           value = checkTF(value);
 304           break;
 305         case "showconservation":
 306           prefName = Preferences.SHOW_CONSERVATION;
 307           value = checkTF(value);
 308           break;
 309         case "showgroupconsensus":
 310           prefName = Preferences.SHOW_GROUP_CONSENSUS;
 311           value = checkTF(value);
 312           break;
 313         case "showgroupconservation":
 314           prefName = Preferences.SHOW_GROUP_CONSERVATION;
 315           value = checkTF(value);
 316           break;
 317         case "showoccupancy":
 318           prefName = Preferences.SHOW_OCCUPANCY;
 319           value = checkTF(value);
 320           break;
 321         case "showquality":
 322           prefName = Preferences.SHOW_QUALITY;
 323           value = checkTF(value);
 324           break;
 325         case "showsequencelogo":
 326           prefName = Preferences.SHOW_CONSENSUS_LOGO;
 327           value = checkTF(value);
 328           break;
 329         case "showfeaturegroups":
 330           value = checkTF(value);
 331           break;
 332         case "showfeaturesettings":
 333           value = checkTF(value);
 334           break;
 335         case "showfullid":
 336           value = checkTF(value);
 337           break;
 338         case "showtreebootstraps":
 339           value = checkTF(value);
 340           break;
 341         case "showtreedistances":
 342           value = checkTF(value);
 343           break;
 344         case "showunconserved":
 345           prefName = Preferences.SHOW_UNCONSERVED;
 346           value = checkTF(value);
 347           break;
 348         case "showunlinkedtreenodes":
 349           value = checkTF(value);
 350           break;
 351         default:
 352           if (appletName.startsWith("pdbfile")
 353                   || appletName.startsWith("sequence") && Character.isDigit(
 354                           appletName.charAt(appletName.length() - 1)))
 355           {
 356             // could be pdbFile2, for example
 357             prefName = argName = null;
 358             value = resourcePath + value;
 359             break;
 360           }
 361           // or one of the app preference names
 362           break;
 363         }
 364         // put name and value into application args
 365         if (value != null && argName != null)
 366         {
 367           vargs.add(argName);
 368           if (value != "true")
 369           {
 370             vargs.add(value);
 371           }
 372         }
 373         if (value == null)
 374         {
 375           value = "false";
 376         }
 377         System.out.println("AppletParams propName=" + prefName + " argName="
 378                 + argName + " appletName="
 379                 + appletName + " value=" + value);
 380         if (appletName != null)
 381         {
 382           appletParams.put(appletName, value);
 383         }
 384         if (prefName != null)
 385         {
 386           Cache.setPropertyNoSave(prefName, value);
 387         }
 388       }
 389     }
 390     return appletParams;
 391   }
 392
 393   /**
 394    * Check for a single-argument option.
 395    *
 396    * @param value
 397    * @return "true" or null
 398    */
 399   private static String checkTF(String value)
 400   {
 401     return (value.toLowerCase() == "true" ? "true" : null);
 402   }
 403
 404   /**
 405    * Crude applet innerHTML parser
 406    *
 407    * @param tag
 408    * @param attr
 409    * @return
 410    */
 411   private static String getAttr(String tag, String attr)
 412   {
 413     int pt = tag.indexOf(attr + "=\"");
 414     if (pt < 0)
 415     {
 416       System.out
 417               .println("AppletParams did not read " + attr + " in " + tag);
 418       return null;
 419     }
 420     // <param name="sortByTree" value="True"/>
 421     int pt1 = pt + attr.length() + 2;
 422     int pt2 = tag.indexOf("\"", pt1);
 423     return (pt < 0 ? null : tag.substring(pt1, pt2));
 424   }
 425
 426   public static void main(String[] args)
 427   {
 428     new AppletParams("<applet\r\n"
 429             + "    code=\"jalview.bin.JalviewLite\" width=\"140\" height=\"35\"\r\n"
 430             + "    archive=\"jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar\">  \r\n"
 431             + "  <param name=\"permissions\" value=\"sandbox\"/>\r\n"
 432             + "  <param name=\"file\" value=\"uniref50.fa\"/>\r\n"
 433             + "  <param name=\"treeFile\" value=\"ferredoxin.nw\"/>\r\n"
 434             + "  <param name=\"userDefinedColour\" value=\"C=yellow; R,K,H=FF5555; D,E=5555FF\"/>\r\n"
 435             + "  <param name=\"sortByTree\" value=\"True\"/>\r\n"
 436             + "  <param name=\"showSequenceLogo\" value=\"true\"/>\r\n"
 437             + "  <param name=\"showGroupConsensus\" value=\"true\"/>\r\n"
 438             + "  <param name=\"showFullId\" value=\"false\"/>\r\n"
 439             + "    <param name=\"linkLabel_1\" value=\"Uniprot\"/>\r\n"
 440             + "    <param name=\"linkUrl_1\" value=\"http://www.uniprot.org/uniprot/$SEQUENCE_ID$\"/>\r\n"
 441             + "    <param name=\"linkLabel_2\" value=\"EMBL-EBI Search\"/>\r\n"
 442             + "    <param name=\"linkUrl_2\" value=\"http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$\"/>\r\n"
 443             + "    <param name=\"APPLICATION_URL\" value=\"http://www.jalview.org/services/launchApp\"/>\r\n"
 444             + "     </applet>");
 445   }
 446
 447 }